def get_config_file(config_folder=".", queue_script="vaspjob.pbs"):
"""
Get the file name of the config file in config_folder and its sub-folders
Parameter
config_folder: str (path like)
The folder containing the config file or containing config file in its sub-folder
queue_script: str (filename like)
The filename of the queue script
Return
config_file: dict
The dict of the filename(key) and corresponding path(value).
If the config file is not in config_folder, store None.
If more than one file (the same filename), it will store the uppest file [Ref. get_shortest_path]
"""
config_file = {}
required_file = ["db.json", "my_launchpad.yaml"]
option_file = ["FW_config.yaml", "my_fworker.yaml", "my_qadapter.yaml", queue_script]
files = required_file + option_file
for file in files:
file_list = recursive_glob(config_folder, file)
if len(file_list) == 0:
if file in required_file:
raise FileNotFoundError("{} file is required for configuration of dfttk.".format(file))
else:
warnings.warn("{} file does not exist, the default setting will be used.".format(file))
config_file[file] = None
else:
config_file[file] = get_abspath(get_shortest_path(file_list))
return config_file
def __init__(self, **kwargs):
super(ConfigTemplate, self).__init__()
#The input should be a dict
PATH_TO_STORE_CONFIG = kwargs.get("path_to_store_config", ".")
PATH_TO_STORE_CONFIG = get_abspath(PATH_TO_STORE_CONFIG)
self.PATH_TO_STORE_CONFIG = PATH_TO_STORE_CONFIG
self.VASP_CMD = kwargs.get("vasp_cmd", "mpirun vasp_std")
self.NNODES = kwargs.get("nodes", 1)
self.PPNODE = kwargs.get("ppn", 24)
self.WALLTIME = kwargs.get("walltime", "48:00:00")
self.QUEUE = kwargs.get("queue", "open")
self.PMEM = kwargs.get("pmem", "8gb")
self.PRE_ROCKET = kwargs.get("pre_rocket",
"module load intel impi vasp")
self.POST_ROCKET = kwargs.get("post_rocket", "null")
def handle_potcar_gz(psp_dir=None,
path_to_store_psp="psp_pymatgen",
aci=True,
vasp_cmd="vasp_std",
template="vaspjob.pbs",
queue_type="pbs"):
"""
Compress and move the pseudopotential to a specified path(path_to_store_psp)
(The compress is done by running "pmg config -p psp_dir path_to_store_psp" command)
Parameter
psp_dir: str (path-like)
The origial path containing psp. Both original and uncompressed are ok.
The name of the compressed file or the sub-folder containing psps must be in the following list
["potpaw_PBE", "POT_GGA_PAW_PBE","potpaw_PBE_52", "POT_GGA_PAW_PBE_52","potpaw_PBE_54", "POT_GGA_PAW_PBE_54",
"potpaw_PBE.52", "POT_GGA_PAW_PBE_52","potpaw_PBE.54", "POT_GGA_PAW_PBE_54","potpaw_LDA", "POT_LDA_PAW",
"potpaw_LDA.52", "POT_LDA_PAW_52","potpaw_LDA.54", "POT_LDA_PAW_54","potpaw_LDA_52", "POT_LDA_PAW_52",
"potpaw_LDA_54", "POT_LDA_PAW_54","potUSPP_LDA", "POT_LDA_US","potpaw_GGA", "POT_GGA_PAW_PW91",
"potUSPP_GGA", "POT_GGA_US_PW91"]
For more details, Ref:https://pymatgen.org/installation.html#potcar-setup
The example of the structure of the psp_dir:
e.g. psp_dir
├── potpaw_LDA.54.tar.gz
└── potpaw_PBE.54.tar.gz
or: psp_dir
├── potpaw_LDA_54
│ ├── Ac
│ ├── Ag
│ └── ...
├── potpaw_PBE_54
│ ├── Ac
│ ├── Ag
│ └── ...
└── ...
path_to_store_psp: str (path-like)
The destination to store the compressed psp. Default: psp_pymatgen
Return
None
"""
def copy_potcar(psp_dir,
psp_uncompress,
aci_name_map={"USPP_GAA": "POT_GGA_US_PW91"}):
flag_copy = False
for potcar_path in psp_dir:
if not os.path.exists(potcar_path):
continue
file_str = os.listdir(potcar_path)
for file_i in file_str:
dst_path_name = parse_psp_name(file_i)
if not (dst_path_name or file_i in aci_name_map):
continue
if file_i in aci_name_map:
dst_path_name = aci_name_map[file_i]
psp_old = os.path.join(potcar_path, file_i)
psp_new = os.path.join(psp_uncompress, dst_path_name)
if os.path.isdir(psp_old):
if os.path.exists(psp_new):
warnings.warn(
"Potential({}) exists, and current potential will over write it."
.format(psp_new))
shutil.rmtree(psp_new)
flag_copy = True
shutil.copytree(psp_old, psp_new)
else:
creat_folders(psp_new)
if file_i.endswith(".tar.gz") or file_i.endswith(".tgz"):
os.system("tar -zxvf " + psp_old + " -C " + psp_new)
flag_copy = True
elif file_i.endswith(".tar"):
os.system("tar -xvf " + psp_old + " -C " + psp_new)
flag_copy = True
else:
warnings.warn(
"Current file ({}) is not supported. The pseudopotential should be uncompressed \
or compressed file endi with .tar.gz or .tgz or .tar"
.format(file_i))
if not flag_copy:
warnings.warn("No supported pseudopotential was found in : {}.".format(", ".join(psp_dir)) + \
"The name rule ref. https://github.com/PhasesResearchLab/dfttk/blob/master/docs/Configuration.md")
return flag_copy
if not psp_dir:
psp_dir = ["pp", "pps", "psp", "potential", "pseudopotential"]
if isinstance(psp_dir, str):
psp_dir = []
aci_name_map = {"USPP_GAA": "POT_GGA_US_PW91"} #A typo in ACI cluster
psp_uncompress = get_abspath("./psp_uncompress")
creat_folders(psp_uncompress)
flag_aci = False
if aci:
#For ACI at PSU only
aci_pp_path = find_psppath_in_cluster(vasp_cmd=vasp_cmd,
psp_pathnames=psp_dir,
template=template,
queue_type=queue_type)
flag_aci = copy_potcar(aci_pp_path,
psp_uncompress,
aci_name_map=aci_name_map)
# file_str is not abspath, is relative path
flag_user = copy_potcar(psp_dir, psp_uncompress, aci_name_map=aci_name_map)
if not (flag_aci or flag_user):
raise FileNotFoundError(
"No pseudopotential was found, plese provide correct pseudopotential \
and use -psp parameter to point to correct position")
# config the POTCAR
os.system("pmg config -p " + psp_uncompress + " " + path_to_store_psp)
# Remove the uncompress folder
try:
shutil.rmtree(psp_uncompress)
except:
os.system("chmod +w " + os.path.join(psp_uncompress, "*/*"))
shutil.rmtree(psp_uncompress)
